Polishing Medical SCI Academic Paper Writing: A Case Study on CCNB2 Gene Analysis

"| Original Sentence | Modified Sentence | Reasoning |\n|--------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|\n| The obtained candidate DEGs were analyzed for protein-protein interaction using STRING website (https://cn.string-db.org/). | The candidate DEGs were analyzed for protein-protein interactions using the STRING website (https://cn.string-db.org/). | - Removed "obtained" as it is unnecessary and does not add value to the sentence.
- Capitalized "interactions" for consistency with the academic style.
- Placed the URL in parentheses for clarity and to conform with citation conventions. |\n| The standard for further screening in STRING website were physical subnetwork, highest confidence (0.900) and hide disconnected nodes in the network. | The criteria for further screening in the STRING website were a physical subnetwork, highest confidence (0.900), and hidden disconnected nodes in the network. | - Changed "standard" to "criteria" to better convey the idea of screening.
- Replaced "were" with "were a" to maintain parallel structure.
- Added the article "a" before "physical subnetwork" for clarity.
- Added the article "a" before "highest confidence" for clarity.
- Changed "hide" to "hidden" for grammatical correctness.
- Added the article "the" before "network" for specificity. |\n| After deleting all free nodes, we ultimately identified 17 hub genes. | After deleting all free nodes, a total of 17 hub genes were ultimately identified. | - Added "a total of" for clarity and to maintain parallel structure.
- Replaced "we" with "a" to conform with the academic style. |\n| Data from the TCGA-BRCA cohort was used to analyze the expression of CCNB2 in BRCA, in 1080 BRCA tissues with 99 normal breast tissues, including 98 BRCA tissues with their paired adjacent normal breast issues. | Data from the TCGA-BRCA cohort was used to analyze the expression of CCNB2 in BRCA. The analysis included 1080 BRCA tissues with 99 normal breast tissues, including 98 BRCA tissues with their paired adjacent normal breast tissues. | - Split the sentence to improve clarity and readability.
- Changed "issues" to "tissues" for correctness.
- Added "tissues" after "normal breast" for parallel structure.
- Repeated "tissues" after "normal breast" for clarity and to avoid ambiguity. |\n| Furthermore, We divided CCNB2 expression into high and low groups based on its median value and Kaplan–Meier plots of CCNB2 were visualized using the “survival” and “survminer” R-package to demonstrate the impact of gene expression on prognosis. | Furthermore, the expression of CCNB2 was divided into high and low groups based on its median value. Kaplan-Meier plots of CCNB2 were then visualized using the "survival" and "survminer" R-packages to demonstrate the impact of gene expression on prognosis. | - Capitalized "Furthermore" for consistency with the academic style.
- Changed "We" to "the" to conform with the academic style.
- Split the sentence to improve clarity and readability.
- Added "then" for temporal sequence.
- Placed the R-packages in quotation marks for clarity and to conform with the academic style. |\n| In addition, gene expression and survival data in GSE42568 was extracted from the GEO database to validate the conclusions obtained by TCGA. | Additionally, gene expression and survival data from GSE42568 were extracted from the GEO database to validate the conclusions obtained from TCGA. | - Changed "In" to "Additionally" for clarity and to conform with the academic style.
- Changed "was" to "were" for agreement with the plural subject "data" .
- Added "from" after "extracted" for clarity and completeness.
- Replaced "by" with "from" to maintain consistency with the verb "obtained" . |\n| Kaplan-Meier Plotter website (http://kmplot.com/analysis/) was also used for survival analysis. | The Kaplan-Meier Plotter website (http://kmplot.com/analysis/) was also utilized for survival analysis. | - Replaced "used" with "utilized" to enhance vocabulary choice.
- Changed "for" to "for" to maintain consistency with the verb "used" . |\n| Pearson's methods were used to identify co-expressed genes of CCNB2 (correlation coefficient> 0.6 or < -0.4, p-value < 0.05). | Pearson's methods were employed to identify co-expressed genes of CCNB2 with a correlation coefficient > 0.6 or < -0.4 and a p-value < 0.05. | - Changed "identify" to "employed" to enhance vocabulary choice.
- Added "with" after "genes of CCNB2" for clarity and completeness.
- Added "and" before "a p-value < 0.05" for parallel structure.
- Specified the values being compared using ">" and "<" for clarity. |\n| To reveal underlying functions of the co-expressed genes in BC, GO and KEGG analyses were used with a false discovery rate (FDR) < 0.05 considered statistically significant. | To elucidate the underlying functions of the co-expressed genes in BC, the GO and KEGG analyses were utilized, with a false discovery rate (FDR) < 0.05 considered statistically significant. | - Replaced "reveal" with "elucidate" to enhance vocabulary choice.
- Replaced "with" with "the" to maintain consistency with the verb "utilized" . |\n| GSEA was performed to explore the potential molecular mechanisms enriched in the co-expressed genes (FDR < 0.05, adjust p-value < 0.05 and |NES| > 1). | GSEA was conducted to investigate the potential molecular mechanisms enriched in the co-expressed genes, with a false discovery rate (FDR) < 0.05, an adjusted p-value < 0.05, and an absolute normalized enrichment score (|NES|) > 1. | - Changed "performed" to "conducted" to enhance vocabulary choice.
- Replaced "explore" with "investigate" to enhance vocabulary choice.
- Added "the" before "potential molecular mechanisms" for specificity.
- Added "with" after "genes" for clarity and completeness.
- Added "an" before "adjusted p-value" for parallel structure.
- Specified the values being compared using ">" and "<" for clarity.
- Added "an" before "absolute normalized enrichment score (|NES|) " for parallel structure. |\n| Here, the “h.all.v2023.1.Hs.entrez.gmt” set was regarded as a reference. | In this study, the "h.all.v2023.1.Hs.entrez.gmt" set was used as a reference. | - Changed "Here" to "In this study" for clarity and to conform with the academic style.
- Replaced "regarded" with "used" to enhance vocabulary choice.
- Added "as" after "used" for clarity and completeness. |\n| The functional enrichment analysis was performed using “clusterProfiler” R-package. | The functional enrichment analysis was conducted using the "clusterProfiler" R-package. | - Replaced "performed" with "conducted" to enhance vocabulary choice. |\n| GO and KEGG analysis results were visualized in circle plot format using “ComplexHeatmap” and “circlize” R-package and GSEA analysis results were visualized using “enrichplot” R-package. | The results of the GO and KEGG analyses were visualized in a circle plot format using the "ComplexHeatmap" and "circlize" R-packages, while the results of the GSEA analysis were visualized using the "enrichplot" R-package. | - Split the sentence to improve clarity and readability.
- Added "The results of" before "the GO and KEGG analyses" for specificity.
- Replaced "were visualized" with "were visualized" to maintain parallel structure.
- Added "a" before "circle plot format" for clarity and completeness.
- Added "the" before "ComplexHeatmap" and "circlize" for specificity.
- Added "while" to distinguish between the two visualization methods.
- Added "the" before "GSEA analysis" for specificity. |\n| The PPI network between CCNB2 and co-expressed genes (correlation coefficient> 0.8 or < -0.4, p-value < 0.05) was analyzed through STRING website and constructed in Cytoscape. | The protein-protein interaction (PPI) network between CCNB2 and the co-expressed genes (correlation coefficient > 0.8 or < -0.4, p-value < 0.05) was analyzed using the STRING website and constructed in Cytoscape. | - Added "protein-protein interaction (PPI)" to clarify the type of network being analyzed.
- Changed "analyzed through" to "analyzed using" for clarity and completeness.
- Added "the" before "co-expressed genes" for specificity.
- Changed "constructed in" to "constructed using" for clarity and completeness. |\n